Molecular modeling and visualization software: Difference between revisions
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*[http://hollow.sourceforge.net/ HOLLOW] is not a stand-alone molecular visualization program; however, it facilitates the production of surface images of proteins. You input a PDB file and get out a PDB file of dummy water atoms that forms a "cast" of the voids and channels of a protein. | *[http://hollow.sourceforge.net/ HOLLOW] is not a stand-alone molecular visualization program; however, it facilitates the production of surface images of proteins. You input a PDB file and get out a PDB file of dummy water atoms that forms a "cast" of the voids and channels of a protein. | ||
* [http://rinalyzer.de/ RINalyzer] enables analyzing and visualizing residue interaction networks (RINs) constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in [http://www.cytoscape.org/ Cytoscape], in conjunction with the molecular 3D structure visualized in the [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera] visulization/modelling system. [http://www.cytoscape.org/ Cytoscape] is a free, open-source software platform for the analysis and visualization of molecular interaction networks. RIN Data for any PDB entry can be downloaded [http://rinalyzer.de/rindata.php here] using the [[PDB code]], alternatively the [http://protein.cribi.unipd.it/ring/ RING web server] can be used to generate RINs. | * [http://rinalyzer.de/ RINalyzer] enables analyzing and visualizing residue interaction networks (RINs) constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in [http://www.cytoscape.org/ Cytoscape], in conjunction with the molecular 3D structure visualized in the [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera] visulization/modelling system. [http://www.cytoscape.org/ Cytoscape] is a free, open-source software platform for the analysis and visualization of molecular interaction networks. RIN Data for any PDB entry can be downloaded [http://rinalyzer.de/rindata.php here] using the [[PDB code]], alternatively the [http://protein.cribi.unipd.it/ring/ RING web server] can be used to generate RINs. | ||
* [http://qutemol.sourceforge.net/ Qutemol] is an open source (GPL), interactive, high quality molecular visualization system. QuteMol produces images in real time by running algorithms that rely on modern graphic card features, including programmable fragment & vertex shaders, and frame and vertex buffer objects. | * [http://qutemol.sourceforge.net/ Qutemol] is an open source (GPL), interactive, high quality molecular visualization system. QuteMol produces images in real time by running algorithms that rely on modern graphic card features, including programmable fragment & vertex shaders, and frame and vertex buffer objects. Other molecular visualization software has also been developed to take advantage of the current generation of high powered video graphic cards or graphic processing units (GPUs), see [http://www.ncbi.nlm.nih.gov/pubmed/21310717 Chavent et al. 2011. GPU-powered tools boost molecular visualization.]. | ||
==Free molecular modeling software== | ==Free molecular modeling software== | ||
